Gene loci information

Transcript annotation

  • This transcript has been annotated as Tight junction protein ZO-1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g2239 g2239.t2 isoform g2239.t2 16241573 16248919
chr_3 g2239 g2239.t2 exon g2239.t2.exon1 16241573 16242028
chr_3 g2239 g2239.t2 cds g2239.t2.CDS1 16241573 16242028
chr_3 g2239 g2239.t2 exon g2239.t2.exon2 16242291 16244277
chr_3 g2239 g2239.t2 cds g2239.t2.CDS2 16242291 16244277
chr_3 g2239 g2239.t2 exon g2239.t2.exon3 16244342 16244436
chr_3 g2239 g2239.t2 cds g2239.t2.CDS3 16244342 16244436
chr_3 g2239 g2239.t2 exon g2239.t2.exon4 16244507 16244581
chr_3 g2239 g2239.t2 cds g2239.t2.CDS4 16244507 16244581
chr_3 g2239 g2239.t2 exon g2239.t2.exon5 16248848 16248919
chr_3 g2239 g2239.t2 cds g2239.t2.CDS5 16248848 16248919
chr_3 g2239 g2239.t2 TSS g2239.t2 16249512 16249512
chr_3 g2239 g2239.t2 TTS g2239.t2 NA NA

Sequences

>g2239.t2 Gene=g2239 Length=2685
ATGGATAGCCTTCTTAATACAAGTGCACATAATGGACAACAGTTACCAAATAATCACTTC
TTGGATCCCCAGGGCGAGAGAACTTCATGGGAATATCACACTGTGATTTTATTCAGAGTT
GCTGGATATGGTTTTGGCATCGCTGTGTCGGGTGGAAGAGATAATCCGCATTTTGCTAAT
GGAGATCCCTCGATTGCAGTTAGTGATGTGCTTAAAGGTGGTCCAGCAGAGGGAAAACTT
GAAACAAACGATCGAATAATAACAGCAAATGGAATCTCATTGGAAAATGTTGAATATGCA
ACAGCAGTTCAAGTTTTAAGAGATAGTGGCAATACAGTGACACTTGTTGTTAAAAGACGT
GCACCATTGCAATCAAGTGGAAATTATCAACAAGCTGGTATCAGTAATAGTGCAATTCCA
ACTCATCAGCATCAGCAAAGTCTCAGTTCAATCGGATCTCAACAGCAAATTAAACTTGTC
ATCAATAAGAGCAGTAAGAAAGAAGATTTTGGAATCGTTCTTGGCTGTAGATTATTCATC
AAAGAGATCTCATCGAAAACACGTGAGCAACTTGCACTTAATGGTTACTCACTGCAAGAA
GGTGACATTGTTACTCGAGTTCATAATACAAATTGCAATGACATGATGAGCATAAAGGAA
GCAAGAAAAATTATGGATAGTTGCAAAGAACGATTAAATCTTGCTGTAATAAGAGATCCA
AATGCAATAGTGCCACCACCTCAGCCAAACACTTCAATTTACTCTCATCAACAGCAAATG
TCAAATTGCTCGAATATCGAAGATGCTTTCAATTCATCAGCTTATTCAACACAGAATCTC
TATGTGCAACCACCAACTAGACCATCATTAAGCACATTACTTGATGACAAGTGCAATCTT
ACACCACGAGGTAGAGCTCGAGGACCAATAACTGATATGTCACAGCTTTCACAACTTGAT
CGTCCATCATCACCACCTCATCATTCAAGAAGTCGTAGTGGAATTGAAATGATAGATGAA
CCGCCTCGACCGCCACCACCTCGTGATGAATTTTATGGCACAAGACGAATGCAAGCAGAA
ACGACTGAACCAAGATATATTACATTCCAGAAAGAAGGTTCTGTTGGTATCAGACTAACA
GGTGGCAATGAAGTTGGAATTTTTGTGACTGCAGTTCAACAAAATAGTCCAGCATCAATG
CAAGGACTTGTGCCTGGTGATAAATTGCTAAAAGTTAATGACATGGATATGAATGGAGTG
ACTAGAGAAGAAGCAGTTTTATTCCTTCTTTCACTTCAAGACCGCATTGATTTAATTGTG
CAATATTGCAAAGATGAATATGAAAATGTCGTTCAAAATCAACGTGGTGATTCATTTCAT
ATTAAGACACATTTTCATTATGATGCTCCAACCAAGAATGAACTTTCATTTAAATCAGGT
GATGTGTTTAGAGTGATTGATACTCTTCACAATGGAGTTGTCGGTTCATGGCAAGTTATG
AGAATTGGAAGAGGACAACAAGAACTTCAGCGTGGAATCATTCCAAATAAAGCAAGAGCT
GAAGAACTTGCAACAGCTCAGTTTAATGCTACAAAGAAAGAAACAACAAATACAGAATCA
AGAATGAATTTCTTTAGACGTAAAAGAACAAATCATCGCAGATCGAAGTCTTTATCACGT
GAAAATTGGGATGATGTTGTTTTTGCTGATTCAGTCTCGAAATTCCCAGCTTATGAACGA
GTTGTTTTAAGACACCCAGGATTCATTCGTCCAGTAGTTTTATTTGGACCAGTTGCAGAT
CTCGCTAGAGAAAGATTGATCAAAGATCATCCAGAAAAGTTTACAGCACCATTACAAGAT
ACTGATAAATCAAAATGTGGTATTGTCAGATTGTCAAATATTCGTGACATTATGGATAGA
GGAAAGCATGCATTACTTGATATCACACCAAATGCAGTTGATCGTCTGAATTATGCTCAA
TTTTATCCAATTGTTGTGTTTTTGAAAGCCGATTCAAAGCATACAATTAAACAATTGCGA
CAAGGTATTCCAAAAACAGCACACAAAAGTTCAAAGAAACTTTTTGAGCAATGCCAGAAA
CTTGATCGAATGTGGTCACATGTGTTTAGCACTACAATTAATTTAAATGATGCAGAATCG
TGGTATCGAAAAACTAAAGAGACTGTCGATAAGCAACAAGCTGGTGCTGTGTGGATGTCA
GAGACAAAGGAATCAAGATTTACCTCAGATATTTTTCTTCCTTATTTATCACCGCCATTA
TGTCCTTATGCTTGTTGTAATCCAACACGTCCGAGAGTTCATGTTGCTAGTTCATTAGCT
TATTATCAAAGGCCTCGCTATTCTATGCAATTGCCTGCTCCTGTGAATTATCAGATTGTT
CCGATTCGTCACTCAAATAGCTTTTATCGAACGCCAACAAGAAGCTTACAAAGTTTAAAT
ACTTTTGGCAATTTCCGTGCAATTGATGATAATAATAATAGCTCGCGTACTGGAACTCTG
AGAAATCACAATGAAGAGCGTAAATCGCCATATTATTATAATGAACTAACTCAAATGCAT
GCAACTAATCCGCAACAACAATTTATACCAATTACTAATCACATTAATGATGATAACTTT
ACAGATTTCATTAATACCATTCATCATTCTGAAACAATGTCATGA

>g2239.t2 Gene=g2239 Length=894
MDSLLNTSAHNGQQLPNNHFLDPQGERTSWEYHTVILFRVAGYGFGIAVSGGRDNPHFAN
GDPSIAVSDVLKGGPAEGKLETNDRIITANGISLENVEYATAVQVLRDSGNTVTLVVKRR
APLQSSGNYQQAGISNSAIPTHQHQQSLSSIGSQQQIKLVINKSSKKEDFGIVLGCRLFI
KEISSKTREQLALNGYSLQEGDIVTRVHNTNCNDMMSIKEARKIMDSCKERLNLAVIRDP
NAIVPPPQPNTSIYSHQQQMSNCSNIEDAFNSSAYSTQNLYVQPPTRPSLSTLLDDKCNL
TPRGRARGPITDMSQLSQLDRPSSPPHHSRSRSGIEMIDEPPRPPPPRDEFYGTRRMQAE
TTEPRYITFQKEGSVGIRLTGGNEVGIFVTAVQQNSPASMQGLVPGDKLLKVNDMDMNGV
TREEAVLFLLSLQDRIDLIVQYCKDEYENVVQNQRGDSFHIKTHFHYDAPTKNELSFKSG
DVFRVIDTLHNGVVGSWQVMRIGRGQQELQRGIIPNKARAEELATAQFNATKKETTNTES
RMNFFRRKRTNHRRSKSLSRENWDDVVFADSVSKFPAYERVVLRHPGFIRPVVLFGPVAD
LARERLIKDHPEKFTAPLQDTDKSKCGIVRLSNIRDIMDRGKHALLDITPNAVDRLNYAQ
FYPIVVFLKADSKHTIKQLRQGIPKTAHKSSKKLFEQCQKLDRMWSHVFSTTINLNDAES
WYRKTKETVDKQQAGAVWMSETKESRFTSDIFLPYLSPPLCPYACCNPTRPRVHVASSLA
YYQRPRYSMQLPAPVNYQIVPIRHSNSFYRTPTRSLQSLNTFGNFRAIDDNNNSSRTGTL
RNHNEERKSPYYYNELTQMHATNPQQQFIPITNHINDDNFTDFINTIHHSETMS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g2239.t2 CDD cd00992 PDZ_signaling 33 118 1.58186E-19
17 g2239.t2 CDD cd00992 PDZ_signaling 364 441 1.14861E-17
19 g2239.t2 CDD cd11859 SH3_ZO 460 521 1.48926E-34
15 g2239.t2 Gene3D G3DSA:2.30.42.10 - 22 131 7.4E-28
14 g2239.t2 Gene3D G3DSA:2.30.42.10 - 139 243 1.7E-6
16 g2239.t2 Gene3D G3DSA:2.30.42.10 - 351 458 9.2E-25
13 g2239.t2 Gene3D G3DSA:2.30.30.40 SH3 Domains 459 741 1.4E-93
12 g2239.t2 Gene3D G3DSA:3.40.50.300 - 587 733 1.4E-93
26 g2239.t2 MobiDBLite mobidb-lite consensus disorder prediction 286 346 -
27 g2239.t2 MobiDBLite mobidb-lite consensus disorder prediction 311 330 -
25 g2239.t2 MobiDBLite mobidb-lite consensus disorder prediction 332 346 -
5 g2239.t2 PANTHER PTHR13865 TIGHT JUNCTION PROTEIN 10 818 0.0
6 g2239.t2 PANTHER PTHR13865:SF28 POLYCHAETOID, ISOFORM O 10 818 0.0
4 g2239.t2 Pfam PF00595 PDZ domain 35 117 6.4E-15
3 g2239.t2 Pfam PF00595 PDZ domain 371 441 2.7E-12
1 g2239.t2 Pfam PF07653 Variant SH3 domain 460 521 6.1E-10
2 g2239.t2 Pfam PF00625 Guanylate kinase 632 731 3.3E-12
31 g2239.t2 ProSiteProfiles PS50106 PDZ domain profile. 34 121 19.561
32 g2239.t2 ProSiteProfiles PS50106 PDZ domain profile. 158 240 9.994
30 g2239.t2 ProSiteProfiles PS50106 PDZ domain profile. 371 444 15.702
29 g2239.t2 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 456 524 12.504
28 g2239.t2 ProSiteProfiles PS50052 Guanylate kinase-like domain profile. 629 730 16.611
22 g2239.t2 SMART SM00228 pdz_new 43 121 2.0E-14
21 g2239.t2 SMART SM00228 pdz_new 168 240 1.1
20 g2239.t2 SMART SM00228 pdz_new 373 444 3.0E-17
23 g2239.t2 SMART SM00326 SH3_2 459 523 0.0046
24 g2239.t2 SMART SM00072 gk_7 552 733 3.1E-40
7 g2239.t2 SUPERFAMILY SSF50156 PDZ domain-like 18 121 5.32E-22
8 g2239.t2 SUPERFAMILY SSF50156 PDZ domain-like 144 246 1.46E-6
9 g2239.t2 SUPERFAMILY SSF50156 PDZ domain-like 359 458 2.4E-26
11 g2239.t2 SUPERFAMILY SSF50044 SH3-domain 459 524 3.54E-10
10 g2239.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 631 740 1.27E-15

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values